#! /bin/sh# Frequently when searching for a transition state, one needs an accurate second# derivatives matrix, a Hessian. An exact Hessian may be obtained analytically# but this may be very expensive for large molecules. In such cases it may be# beneficial to calculate Hessian matrix elements only for atoms directly# involved in the reaction for which a transition state is sought for. The rest# of the Hessian can then be approximated using a cheaper method.# In this example, a saddle point of the ethane internal rotation around C-C# bond is found. In principle, only hydrogen atoms contribute to the normal mode# we are interested in. Therefore we calculate a partial Hessian matrix# including hydrogen atoms only. For this purpose, the AnalyticalFreq block key# is used. In this block, a NUC keyword is added specifying that the second# derivatives are calculated for atom 3 (and its symmetry-equivalents) only.# Note that the Hessian matrix elements between symmetry-equivalent atoms, for# example between 3,H and 4.H are also calculated. The rest of the matrix is# estimated using the default method."$ADFBIN/adf"<<eorTITLE Ethane transition state search using partial HessianATOMS1 C 0.000000000000 0.000000000000 0.767685465031 2 C 0.000000000000 0.000000000000 -0.767685465031 3 H 0.964354016767 0.347635559279 1.177128271450 4 H -0.181115782790 -1.008972856410 1.177128271450 5 H -0.783238233981 0.661337297125 1.177128271450 6 H -0.500471876676 0.894626767091 -1.177128271450 7 H -0.524533568868 -0.880734742626 -1.177128271450 8 H 1.025005445540 -0.013892024465 -1.177128271450 ENDBASIStype DZcore LargeENDAnalyticalFreq NUC 3EndBeckeGrid quality goodEndeor
rm TAPE13
mv TAPE21 ethane-frq.t21
# After the Hessian is calculated, the resulting TAPE21 file is used for a# subsequent transition state search:"$ADFBIN/adf"<<eorTITLE Ethane transition state search using partial HessianATOMS1 C 0.000000000000 0.000000000000 0.767685465031 2 C 0.000000000000 0.000000000000 -0.767685465031 3 H 0.964354016767 0.347635559279 1.177128271450 4 H -0.181115782790 -1.008972856410 1.177128271450 5 H -0.783238233981 0.661337297125 1.177128271450 6 H -0.500471876676 0.894626767091 -1.177128271450 7 H -0.524533568868 -0.880734742626 -1.177128271450 8 H 1.025005445540 -0.013892024465 -1.177128271450 ENDFragments H t21.H C t21.CENDGEOMETRY transitionstate mode=1 iterations 30 step rad=0.15 hessupd BOFILL converge e=1.0e-4 grad=1.0e-4 rad=1.0e-3ENDRESTART File ethane-frq.t21EndBeckeGrid quality goodEndeor# Important note: care should be taken to specify correct mode in the# TransitionState keyword. Because a significant part of the Hessian will not be# calculated exactly, it is possible that it will have more than one negative# eigenvalue, in which case the one we are interested in may not be the first# one. In such a case, one needs to specify the correct mode number in the# TransitionState keyword.